Winchester College headmaster W. F. Oakeshott discovered a previously unknown manuscript copy of the work in June 1934, during the cataloging of the college's library. Newspaper accounts announced that what Caxton had published in 1485 was not exactly what Malory had written. Oakeshott published “The Finding of the Manuscript” in 1963, chronicling the initial event and his realization that “this indeed was Malory,” with “startling evidence of revision” in the Caxton edition. It is hypothesized that Caxton's text and the Winchester manuscript are both derived from an earlier copy. (Having said this, microscopic examination revealed that ink smudges on the Winchester manuscript are offsets of newly printed pages set in Caxton's own font, which indicates that the Winchester Manuscript was in Caxton's print shop.) The “Winchester Manuscript” is believed to be closer on the whole to Malory's original. In addition, it does not have the book and chapter divisions for which Caxton takes credit in his preface.
Malory scholar Eugène Vinaver examined the manuscript shortly after its discovery. Oakeshott was encouraged to produce an edition himself, but he ceded the project to Vinaver. Based on his initial study of the manuscript, Oakeshott concluded in 1935 that the copy from which Caxton printed his edition “was already subdivided into books and sections.” Vinaver made an exhaustive comparison of the manuscript with Caxton's edition and reached similar conclusions. In his 1947 publication of The Works of Sir Thomas Malory, he argued that Malory did not write a single book, but rather a series of Arthurian tales, each of which is an internally consistent and independent work. However, scholars (including William Matthews) pointed out that Malory's later tales make frequent references back to the earlier events, suggesting that he had wanted the tales to cohere better but had not sufficiently revised the whole text to achieve this.
The Winchester manuscript has been digitised by a Japanese team, who note that "the text is imperfect, as the manuscript lacks the first and last quires and few leaves. The most striking feature of the manuscript is the extensive use of red ink."